Inhibition of quorum sensing-mediated processes in bacteria

ABSTRACT

Methods are provided for identifying molecules that can be used to positively and negatively manipulate quorum-sensing-mediated communication to control bacterial behavior. Small-molecule antagonists that disrupt quorum-sensing-mediated activities are identified. Methods are provided for disrupting detection of acyl-homoserine lactone autoinducer in Gram-negative bacteria by contacting the bacteria with the antagonists. Methods of inhibiting quorum sensing-mediated activity in Gram-negative bacteria are provided wherein the activity is pathogenicity, bioluminescence, siderophore production, type III secretion, or metalloprotease production.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application claims priority to U.S. Provisional Application No. 61/130,685, filed Jun. 2, 2008 and U.S. Provisional Application No. 61/188,310, filed Aug. 7, 2008, both of which are herein incorporated in their entirety, by reference.

STATEMENT OF GOVERNMENT INTEREST

This invention was made with government support under grant 5R01GM065859 and grant 5R01 AI 054442 from the National Institutes of Health and grant MCB-0343821 from the National Science Foundation. The federal government has certain rights in the invention.

The antagonist screen was partly funded with federal funds supplied to the National Cancer Institute's Initiative for Chemical Genetics, National Institutes of Health, under Contract No. N01-CO-12400 and has been performed with the assistance of the Chemical Biology Platform of the Broad Institute of Harvard and MIT. The content of this publication does not necessarily reflect the views or policies of the Department of Health and Human Service, nor does mention of trade names, commercial products or organizations imply endorsement by the U.S. Government.

FIELD OF THE INVENTION

This invention relates to quorum sensing activities, and more particularly to antagonists of the receptor for acyl-homoserine lactone-type autoinducer molecules. In particular, the invention provides novel small molecules and methods of use of those molecules for controlling bacterial growth and pathogenesis.

BACKGROUND OF THE INVENTION

Quorum sensing is a process of bacterial cell-cell communication that involves production and detection of secreted signaling molecules called autoinducers (AI). Quorum sensing allows bacteria to collectively regulate gene expression and thereby function as multi-cellular organisms. For example, the bioluminescent Gram-negative quorum-sensing bacterium Vibrio harveyi integrates information from three different diffusible autoinducers that together enable intra- and inter-species communication. The three V. harveyi autoinducers are AI-1 (3-hydroxybutanoyl homoserine lactone), AI-2 ((2S,4S)-2-methyl-2,3,3,4-tetrahydroxytetrahydrofuran-borate), and CAI-1 ((S′)-3-hydroxytridecan-4-one). These signals are detected by the sensor-kinase proteins, LuxN, LuxQ, and CqsS, respectively (FIG. 1A) (Henke, J. M., and Bassler, B. L. (2004b). J Bacteriol 186, 6902-6914). At low cell density, (i.e., in the absence of autoinducers), these sensor kinases autophosphorylate and transfer phosphate to the shared phospho-transfer protein, LuxU. LuxU transfers the phosphoryl-group to the DNA-binding response regulator, LuxO, which activates transcription of genes encoding five redundant small regulatory RNAs called the quorum regulatory RNAs (Qrrs) (FIG. 1A). The Qrrs destabilize the mRNA transcript encoding the master quorum-sensing regulator, LuxR. Therefore, under low-cell-density conditions, the bacteria do not display quorum-sensing behaviors. In contrast, at high cell density the three autoinducers accumulate and bind to their cognate receptors. These binding events switch the receptors to phosphatases, resulting in dephosphorylation of LuxO and termination of Qrr production. The luxR transcript is stabilized, leading to LuxR protein production (FIG. 1A). LuxR controls the genes in quorum sensing, e.g., genes required for bioluminescence, siderophore production, type III secretion, and metalloprotease production (Fuqua, C., Winans, S. C., and Greenberg, E. P. (1996). Annu Rev Microbiol 50, 727-751; Hammer, B. K., and Bassler, B. L. (2003). Mol Microbiol 50, 101-104; Henke, J. M., and Bassler, B. L. (2004a). J Bacteriol 186, 3794-3805; McFall-Ngai, M. J., and Ruby, E. G. (2000). Curr Opin Microbiol 3, 603-607; Miller, M. B., and Bassler, B. L. (2001). Annu Rev Microbiol 55, 165-199; Waters, C. M., and Bassler, B. L. (2005). Annu Rev Cell Dev Biol 21, 319-346).

AI-1 is an acyl homoserine lactone (AHL) type autoinducer and it is the strongest of the three V. harveyi signals and, thus, the major input controlling quorum-sensing-regulated behaviors. Typically, AHL autoinducers are detected by cytoplasmic LuxR-type transcriptional activators (note: these LuxR-type proteins are unrelated to V. harveyi LuxR, FIG. 1A). V. harveyi is unusual because all three of its autoinducers, including AI-1, are detected by membrane-bound sensor-kinase proteins (in the case of AI-2, however, an additional periplasmic binding protein LuxP is required in conjunction with the membrane-bound two-component protein LuxQ). AI-1 is also the defining member of a growing family of recognized AHL type autoinducers that interact with membrane-bound sensor-kinases like LuxN, rather than with cytosolic LuxR-type proteins (Freeman, J. A., et al. (2000). Mol Microbiol 35, 139-149; Jung, K., et al. (2007). J Bacteriol 189, 2945-2948; Timmen, M., et al. (2006). J Biol Chem 281, 24398-24404). There are currently 11 LuxN homologs in the National Center for Biotechnology Information (NCBI) database, but nothing is known about how AHLs interact with this important class of receptors (FIG. 2).

Bacteria that use the AI-1 signaling factor associate with higher organisms, i.e., plants and animals, at some point during their life cycles. Some examples include Pseudomonas aeruginosa, Erwinia carotovora, Pseudomonas aureofaciens, Yersinia enterocolitica, V. harveyi, and agrobacterium tumefaciens. P. aeruginosa is an opportunistic pathogen in humans with cystic fibrosis. E. carotovora infects certain plants and results in soft rot disease. Y. enterocolitica causes gastrointestinal disease in humans and reportedly produces an autoinducer. P. aureofaciens synthesizes antibiotics under autoinducer control that block fungus growth in the roots.

Quorum sensing takes place not only among luminous marine bacteria like V. harveyi, but also among pathogenic bacteria where it regulates the production of virulence factors. Thus, it would be an advance to identify compounds useful for controlling pathogenic bacteria, and for augmenting traditional antibiotic treatments.

SUMMARY OF THE INVENTION

The present invention provides molecules that can be used to positively and negatively manipulate quorum-sensing-mediated communication to control bacterial behavior. Fifteen small-molecules were identified.

Accordingly, in a first aspect, the invention features a small molecule compound characterized by its ability to bind to Vibrio harveyi LuxN at the autoinducer-1 (AI-1) binding site of LuxN, wherein the compound is not AI-1. The isolated compound is one embodiment of the invention.

In a preferred embodiment, the compound is one of the small molecules from the group consisting of the fifteen structures shown in FIG. 3. The compound is an antagonist of V. harveyi LuxN.

In a related aspect, the invention features a method of disrupting detection of acyl-homoserine lactone autoinducer in Gram-negative bacteria comprising contacting the bacteria with the small molecule compound.

In another related aspect, the invention features a pharmaceutical composition comprising a pharmaceutically acceptable carrier, excipient or diluent and one or more of the compounds selected from the group consisting of the fifteen structures shown in FIG. 3.

In a further related aspect, the invention features a method of inhibiting bacterial infection of a host comprising contacting the bacteria with the pharmaceutical composition, wherein the bacteria are Gram-negative quorum sensing bacteria. “Contacting the bacteria” is by means of administering the composition to the host, which can be topical administration or administration to the host internally by means known in the art.

In yet another related aspect, the invention features a bacterial biofilm-inhibiting composition comprising one or more compounds selected from the group consisting of the fifteen structures shown in FIG. 3. In a preferred embodiment the composition also comprises DMSO.

In still another related aspect, the invention features a method of controlling growth of quorum sensing Gram-negative bacteria attached to a solid surface, comprising exposing the bacteria to the bacterial biofilm-inhibiting composition.

A related aspect of the invention features a method of preventing biofilm formation on a solid surface comprising administering the bacterial biofilm-inhibiting composition to the surface.

Another aspect of the invention features a method of inhibiting quorum sensing-mediated activity in Gram-negative bacteria comprising contacting the bacteria with the antagonist compound selected from the group consisting of the fifteen structures shown in FIG. 3.

In a preferred embodiment, the quorum sensing-mediated activity is pathogenicity. In another embodiment the bacteria are pathogenic to humans, animals, or plants. In another embodiment the bacteria are pathogenic to marine life. In a particularly preferred embodiment the activity is pathogenicity and the bacterial species is selected from V. harveyi and C. violaceum.

In another preferred embodiment, the activity is bioluminescence, siderophore production, type III secretion, or metalloprotease production.

Another aspect of the invention features a use of one or more of the compounds from the group consisting of the fifteen structures (A-O) in FIG. 3 for preparation of a medicament for treatment of a bacterial infection wherein the bacteria are Gram-negative quorum sensing bacteria.

Yet another aspect of the invention features a medical device that is coated with one more of the compounds from the group consisting of the fifteen structures (A-O) in FIG. 3. In a preferred embodiment the device is a catheter.

Additional features and advantages of the present invention will be better understood by reference to the drawings, detailed description and examples that follow.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1. The V. harveyi Quorum-Sensing Circuit and the LuxN Trans-Membrane Domain.

(A) CAI-1 is (S)-3-hydroxytridecan-4-one (squares), AI-1 is 3-hydroxybutanoyl homoserine lactone (circles), and AI-2 is (2S,4S)-2-methyl-2,3,3,4-tetrahydroxytetrahydrofuran-borate (triangles), and they are synthesized by CqsA, LuxM, and LuxS, respectively. At low cell densities, in the absence of appreciable autoinducer, CqsS, LuxN, and LuxQ act as kinases funneling phosphate via LuxU to LuxO (arrows). Phospho-LuxO activates expression of the qrr genes; the Qrr sRNAs (comb shapes) are transcribed and they bind to and facilitate the degradation of the mRNA encoding LuxR. Without LuxR, there is no quorum sensing, and thus no light production. At high cell density, in the presence of autoinducers, the receptors act as phosphatases, draining phosphate from LuxO via LuxU. Transcription of the qrr genes is terminated, the LuxR mRNA is stabilized, and LuxR protein is produced. By activating and repressing a variety of genes, LuxR facilitates the transition of the cells into quorum-sensing mode. One operon activated by LuxR at high cell density encodes luciferase, so in the presence of autoinducers, V. harveyi produces light. (B) The cartoon depicts the putative topology of the N-terminal region of LuxN (residues 1-303 of SEQ ID NO:1). Amino acids in the circle, when mutated, confer a dark phenotype. Amino acids in the squares denote sites where mutations enhance sensitivity of LuxN to AI-1. The amino acid in the triangle represents the LuxN* suppressor mutation that prevents C450-0730 antagonism.

FIG. 2. LuxN Sequence Alignment.

V. harveyi LuxN was used to identify other LuxN homologs in the NCBI data base by a basic local alignment comparison. The LuxN homologs were aligned using the Vector NTI AlignX protocol. Dark gray shaded residues indicate a 100% conserved amino acid in all 11 LuxN homologs. Light gray shaded residues indicate that the particular amino acid is greater than 50% conserved.

FIG. 3. Identifying Data for Fifteen Antagonist Molecules.

(A) Antagonist 6807-0002. (B) Antagonist 8008-8157. (C) Antagonist C104-0038. (D) Antagonist C105-2488. (E) Antagonist 3448-8396. (F) Antagonist 3578-0898. (G) Antagonist 3643-3503. (H) Antagonist 4052-1355. (I) Antagonist 4248-0174. (J) Antagonist 4401-0054. (K) Antagonist 4606-4237. (L) Antagonist C137-0541. (M) Antagonist C450-0730. (N) Antagonist C540-0010. (O) Antagonist C646-0078. (P) Table characterizing the molecules pictured in FIG. 3A-3O.

FIG. 4. Molecules that Antagonize LuxN-AI-1 Binding or Signaling.

(A) Structures and designations of five molecules that inhibit LuxN signaling in response to AI-1. The IC₅₀ value for each antagonist molecule is given below its structure. (B) Light production from wild-type LuxN and LuxN F163A was measured at the specified AI-1 concentrations in the presence of 0 μM, 1 μM, and 10 μM C450-0730. Data were fit as described above. (C) The light production values in panel B were collapsed as a function of f−Δε_(WT) as described in Experimental Procedures. f is the ligand-dependent free-energy difference between the kinase active (on) and kinase inactive (off) states of LuxN, and Δε_(WT) is the wild type value of f in the absence of ligand. The binding parameters used are as follows: K_(off) ^(AI-1)==1 nM, K_(on) ^(AI-1)=1 mM, K_(off) ^(C450-0730)=1 mM, K_(on) ^(C450-0730)=500 nM. The collapse was obtained by using Δε−Δε_(WT)=3.2 for the LuxN F163A mutant.

FIG. 5. C. violaceum (wild type) but not the Mutant ΔCviR or ΔCviI are Pathogenic to C. elegans.

The nematode C. elegans was infected with either wild type or mutant C. violaceum bacteria and survival times were recorded. The CviR mutant lacks the cytosolic receptor for the autoinducer. The CviI mutant lacks the autoinducer synthase, so the autoinducer is not produced.

FIG. 6. Representative LuxN Mutations that Reduce Light Production and Increase Qrr Transcription.

(A) Light production and (B) Qrr4 transcript levels at steady state in wild-type and representative LuxN mutants. All cultures were grown and tested in triplicate. Light production from the wild type strain was set as 100%, and light production from each LuxN mutant was normalized to that reference. Qrr transcript levels were measured by qRT-PCR and are reported as relative transcript values. LuxN L138A and LuxN E154Q are control mutants that do not exhibit defects in light production or Qrr transcription.

FIG. 7. LuxN AI-1 Dose-Response Curves.

(A) Light production at various AI-1 concentrations is shown for wild-type LuxN and for representative LuxN mutants that have increased AI-1 EC-50 values. The data were fit with a variable-slope sigmoidal dose-response curve to determine the EC₅₀ values. (B) Light production at various AI-1 concentrations is shown for wild-type LuxN and for representative LuxN mutations that cause constitutive dark phenotypes at all AI-1 concentrations. EC₅₀ values were not determined for these mutants.

FIG. 8. Dose response of LuxN Antagonists.

The concentration of the antagonist molecule is shown on the X-axis, the light output (% lux) is shown on the Y-axis. Squares denote the light output by the double sensor mutant V. harveyi strain JMH624 (ΔluxM, ΔluxPQ) in the presence of 20 nM AI-1 at various concentrations of the antagonist. The chemical structure of the antagonist and the effective concentration (EC₅₀) are given. (A) Antagonist 3448-8396. (B) Antagonist 3578-0898. (C) Antagonist 3643-3503. (D) Antagonist 4248-0174. (E) Antagonist 4401-0054. (F) Antagonist 4606-4237. (G) Antagonist 8008-8157. (H) Antagonist 6807-0002. (I) Antagonist C137-0541. (J) Antagonist C450-0730. (K) Antagonist C540-0010. (L) Antagonist C646-0078.

FIG. 9. AI-1 Dose-response Curves of the LuxN* Suppressor Mutants.

(A) Light production of the wild-type LuxN, the LuxN* mutants, and LuxN F163A at various AI-1 concentrations. The data were fit with a variable-slope sigmoidal dose-response curve to determine the EC₅₀ value for each LuxN* mutant. (B) Light production of the dark LuxN F163A mutant harboring combinations of LuxN* mutations. Data were fit and AI-1 EC₅₀ value was determined as above. An EC₅₀ value could not be determined for the quadruple mutant because it is constitutively bright at all AI-1 concentrations.

FIG. 10. Two Quorum Sensing Mechanisms For Homoserine Lactone Autoinducer Detection.

(A) LuxN is the Vibrio Harveyi transmembrane receptor for autoinducer hydroxybutanoyl homoserine lactone, which requires LuxM synthase for its production. (B) In Chromobacterium violaceum, the synthase CviI is responsible for production of the autoinducer. Autoinducer binds to the cytoplasmic receptor CviR.

FIG. 11. Antagonist Violacein Screen.

Effect of the antagonist molecules on the cytoplasmic LuxR-type receptor (CviR) of Chromobacterium violaceum. Receptor inhibition results in loss of production of the purple pigment violacein. Shown are the violacein readouts of the bacteria in the absence (no HHL) and presence (5 μM HHL) of hydroxybutanoyl homoserine lactone (HHL) and in the presence of the fifteen small molecule antagonists shown.

FIG. 12. C. violaceum (wild type) Pathogenicity is Inhibited by Thiolactone Antagonist.

Survival graphs are shown for C. elegans infected with wild type C. violaceum with or without a supplement of the thiolactone drug 4606-4237.

FIG. 13. C. elegans Survival Times after Infection with C. violaceum Supplemented with Homoserine Lactone, Thiolactone or a Combination of the Two.

Survival graphs are shown for the nematode C. elegans infected with the synthase mutant strain of C. violaceum bacteria in the presence and absence of the homoserine lactone autoinducer and the thiolactone drug 4606-4237.

FIG. 14. LuxN Signal Transduction Can Be Described by a Two-State Model.

(A) Wild-type LuxN toggles between two conformations indicated by the open and closed periplasmic domains. At low cell density, when the AI-1 concentration is negligible, LuxN is strongly biased toward its kinase state represented by the open periplasmic structure. At high cell density, in the presence of AI-1 (dark ovals), LuxN is biased toward the phosphatase state represented by the closed periplasmic structure. (B) This two-state model is represented by a free-energy diagram that describes the two ligand-free forms of the protein as on (open periplasmic domain) or off (closed periplasmic domain). The free energies of these two states are independent of ligand concentration and are represented by horizontal black lines. The free energy of the on state is lower than the free energy of the off state, producing the bias toward the kinase mode at low cell densities (i.e. low autoinducer concentration). The free energy of LuxN in its phosphatase state and bound to ligand (off_(L)) is represented by the descending solid curve. The point at which the free energy of the off_(L) state equals the free energy of the on state (solid circle) corresponds to the EC₅₀ value for AI-1. LuxN mutants identified in the genetic screen that possess increased AI-1 EC₅₀ values are represented as on. Compared to wild-type LuxN, they have lower on state free energies and therefore exhibit larger AI-1 EC₅₀ values. By contrast, the three LuxN* mutants that exhibit a bias toward the phosphatase state are represented as on⁺. These mutants possess higher on state free energies than wild-type LuxN and therefore have decreased AI-1 EC₅₀ values. The EC₅₀ values of the on⁻ and on⁺ mutants are represented by the open circles.

FIG. 15. Data Collapse for LuxN*, LuxN Bias, and Combined LuxN*-Bias Mutants.

(A) Collapse of the dose-response data from LuxN* R245L and G271D mutants with the combined wild-type/LuxN F163A antagonist collapse from FIG. 4C. These LuxN* curves were collapsed by adjusting only the bias Δε−Δε_(WT) to +0.5. (B) Collapse of dose-response curves from representative dark LuxN mutants with the combined wild-type/LuxN F163A antagonist collapse from FIG. 4C. The LuxN W224A and LuxN T214I dose-response curves were collapsed by adjusting only the bias Δε−Δε_(WT) to −1.5 and −4.3, respectively. The LuxN F155A and LuxN F162A dose-response curves were collapsed by adjusting the bias Δε−Δε_(WT) parameter and increasing the K_(off) ^(AI-1): for LuxN F155A, Δε−Δε_(WT)=−1.0 and K_(off) ^(AI-1)=10 nM, for LuxN F162A, Δε−Δε_(WT)=−1.0 and K_(off) ^(AI-1)=100 nM.

DETAILED DESCRIPTION OF THE INVENTION

The novel strategies described herein are aimed at interfering with the detection of quorum sensing molecules known as autoinducers. Quorum sensing controls expression of traits essential for bacterial virulence. Quorum sensing plays a vital role in the pathogenicity of many bacteria because the ability to act as a coordinated group is essential for bacteria to successfully infect host organisms. Interference with either the production or the detection of autoinducer molecules can abolish bacterial communication and render bacteria non-pathogenic. Thus, the novel methods of the present invention, which interfere with bacterial detection of autoinducer are important in controlling populations of bacteria.

The present invention identifies fifteen small molecules that disrupt detection of acyl-homoserine lactone-type autoinducer in Gram-negative bacteria and thus inhibit quorum sensing mediated processes (FIG. 3). These molecules antagonize membrane-bound and cytoplasmic autoinducer receptors. As representative of these two groupings of Gram-negative quorum sensing bacteria, the molecules were demonstrated to act in the model bacterial species Vibrio harveyi and Chromobacterium violaceum by detecting the quorum sensing mediated activities of bioluminescence and violacein production, respectively. V. harveyi is representative of those bacteria that have membrane bound sensor receptor for the autoinducer. C. violaceum is representative of those bacteria that have cytoplasmic sensor receptor for the autoinducer (FIG. 10).

It is known that inhibitors of quorum sensing function to shut down entire pathogenicity regulons. It has been previously shown that use of bioluminescence as a convenient readout activity is an accurate reporter of the inhibition of all other quorum sensing target genes, e.g., virulence factor production, biofilm genes, type III secretion. Published research of Bassler and others in the field have demonstrated that convenient reporters such as bioluminescence, gfp, or violacein production, are accurate representations of what is happening for all the genes in the regulon.

Nonetheless, pathogenicity was studied in more detail in a model system using Caenorhabditis elegans as a model of a host animal infected by pathogenic bacteria. C. violaceum was used as a model of pathogenic bacteria capable of quorum sensing-mediated killing of the host. An antagonist molecule identified from a high-throughput chemical library screen protected C. elegans from quorum sensing-mediated killing by C. violaceum (FIG. 12).

It has previously been shown that the Type III secretion system (TTS) is a quorum sensing mediated activity. TTS systems are specialized secretion apparatuses used by many gram-negative plant and animal pathogens to inject effector virulence factors directly into the cytoplasm of eukaryotic host cells with which they are associated. Once inside the host cell, these effector proteins perform a range of functions that contribute to the propagation of the bacteria. TTS systems have been identified in numerous gram-negative bacterial pathogens, including enteropathogenic Escherichia coli and the marine bacteria Vibrio parahaemolyticus and V. harveyi. In enterohemorrhagic and enteropathogenic Escherichia coli, quorum sensing activates TTS at high cell density (in the presence of autoinducer). In contrast, at high cell density, quorum sensing represses TTS in the marine bacteria V. harveyi and V. parahaemolyticus. (Henke, J. M., and Bassler, B. L. (2004a). J Bacteriol 186, 3794-3805).

Thus, the small molecules of the present invention that have been shown to antagonize the LuxN receptor inhibit quorum sensing activity in E. coli at high cell density and make the bacterium avirulent because the bacterium needs to express TTS late in infection to result in virulence. In Vibrio infection, where TTS is required at low cell density, adding the antagonist small molecule causes the bacteria to express virulence traits at high cell density. This will make the bacterium avirulent because the antagonist will cause the bacterium to express, during late infection, the traits (TTS) that are actually needed early in infection, thus providing non-optimal conditions for infection, causing a growth disadvantage, and wasting energy.

Thus, in a further embodiment, the invention provides a pharmaceutical composition comprising the small molecule compounds of the present invention (FIG. 3), or a pharmaceutically-acceptable salt thereof, and one or more pharmaceutically acceptable carriers, adjuvants or vehicles. The pharmaceutical composition of the invention can be used to treat infections in a warm-blooded animal caused by microorganisms possessing a quorum-sensing mechanism, which comprises administering to the animal a therapeutically effective amount of the pharmaceutical composition of this invention.

The pharmaceutical compositions can be administered by any mode known in the art, including, for example, oral, nasal, topical (including buccal and sublingual) or parenteral (including subcutaneous, intramuscular, intravenous and intradermal) administration. A skilled artisan can determine which form of administration is best and the therapeutic amount in a particular case for balancing the dose needed versus periodic delivery.

Oral administration can include solid dosage forms, such as capsules, tablets, pills, powders, tinctures and granules. In such solid dosage forms, the active compound is generally admixed with at least one inert pharmaceutically acceptable carrier such as sucrose, lactose, or starch. Such dosage forms can also comprise additional substances such as lubricating agents, for example, magnesium stearate. In the case of capsules, tablets and pills, the dosage forms can also comprise buffering agents. Tablets and pills can additionally be prepared with enteric coatings.

Infectious bacteria that use acyl-homoserine lactone quorum sensing strategies to produce virulence include pathogens to humans, animals, and plants. Some pathogens infect marine life and thereafter cause disease in humans who eat or otherwise come into contact with the marine life.

Bacterial infection in humans is facilitated by certain conditions such as burns, wounds, implants or use of a catheter. Chromobacterium violaceum is one species that may infect wounds. Vibrio may contaminate shellfish and cause food poisoning. Individuals with cystic fibrosis (CF) are plagued by bacterial infection of the lungs. Of the several species of bacteria that infect the lungs, Pseudomonas aeroginosa is most problematic.

The invention also provides for a medical device comprising one more of the compounds shown in FIG. 3, wherein the device is supplemented with the compound(s) and the compound is present in a concentration sufficient to disrupt detection of autoinducer-1. The compounds may be coated on the device. As used herein, the term “medical device” means a device having surfaces that contact tissue, blood, or other bodily fluids in the course of their operation. This definition includes within its scope, for example, surgical implants, surgical sutures, wound dressings, extracorporeal devices for use in surgery such as blood oxygenators, blood pumps, blood sensors, tubing used to carry blood and the like which contact blood which is then returned to the subject. The definition includes within its scope endoprostheses implanted in blood contact in a human or animal body such as vascular grafts, stents, pacemaker leads, heart valves, and the like that are implanted in blood vessels or in the heart. The definition also includes within its scope devices for temporary intravascular use such as catheters, guide wires, and the like which are placed into the blood vessels or the heart for purposes of monitoring or repair.

The small molecule compounds of the invention can be used to inhibit bacterial cell growth and biofilm formation on substrates used to manufacture medical devices associated with noninvasive and invasive medical procedures. Such substrates include tubular, sheet, rod and articles of proper shape for use in a number of medical devices such as vascular grafts, aortic grafts, arterial, venous, or vascular tubing, vascular stents, dialysis membranes, tubing or connectors, blood oxygenator tubing or membranes, surgical instruments, ultrafiltration membranes, intra-aortic balloons, stents, blood bags, catheters, sutures, soft or hard tissue prostheses, synthetic prostheses, prosthetic heart valves, tissue adhesives, cardiac pacemaker leads, artificial organs, endotracheal tubes, lenses for the eye such as contact or intraocular lenses, blood handling equipment, apheresis equipment, diagnostic and monitoring catheters and sensors, biosensors, dental devices, drug delivery systems, or bodily implants of any kind. For example, arthroscopic surgery is routinely performed with use of medical devices that minimize the invasiveness of the procedure. Such devices include, for example, ultrathin microfiberoptic endoscopes that offer the laryngologist unique access to the limited spaces of the temporal bone and skull base. In another example, a stent supplemented with a small molecule compound of the invention that deters bacterial infections resulting from the presence of the implanted stent can be constructed. Stents are used to maintain an open lumen in tissues including the tracheo-bronchial system, the biliary hepatic system, the esophageal bowel system, and the urinary tract system. U.S. Pat. No. 5,637,113 issued to Tartaglia, and incorporated herein by reference, teaches a stent with a sheet of polymeric film wrapped around the exterior. With regard to the present invention, the film may be loaded or coated with a small molecule compound or composition of the invention. Alternatively, the material used to manufacture the stent can be impregnated with a small molecule compound or composition of the invention.

A medical device may be further supplemented with, for example, one or more antibodies, analgesics, anticoagulants, anti-inflammatory compounds, antimicrobial compositions, cytokines, drugs, growth factors, interferons, hormones, lipids, demineralized bone or bone morphogenetic proteins, cartilage inducing factors, oligonucleotides polymers, polysaccharides, polypeptides, protease inhibitors, vasoconstrictors or vasodilators, vitamins, minerals, stabilizers and the like. Supplemented, as used herein, includes medical devices that are impregnated, infused, coated, covered, layered, permeated, attached or connected with a small molecule compound or composition of the invention. Methods for immobilizing biomaterials to a medical device are discussed in U.S. Pat. No. 5,925,552, which is incorporated herein by reference. Additional methods of coating surfaces of medical devices with antimicrobial compositions are taught in U.S. Pat. No. 4,895,566 (a medical device substrate carrying a negatively charged group having a pKa of less than 6 and a cationic antibiotic bound to the negatively charged group); U.S. Pat. No. 4,917,686 (antibiotics are dissolved in a swelling agent which is absorbed into the matrix of the surface material of the medical device); U.S. Pat. No. 4,107,121 (constructing the medical device with ionogenic hydrogels, which thereafter absorb or ionically bind antibiotics); U.S. Pat. No. 5,013,306 (laminating an antibiotic to a polymeric surface layer of a medical device); and U.S. Pat. No. 4,952,419 (applying a film of silicone oil to the surface of an implant and then contacting the silicone film bearing surface with antibiotic powders). U.S. Pat. No. 5,902,283 further discloses a method for coating a medical device with an antimicrobial agent such that the agent penetrates the exposed surfaces of the device and is impregnated throughout the material of the device.

It is further envisioned that the small molecule compounds or compositions of the invention can be used to aid wound repair. For example, U.S. Pat. No. 6,117,485 describes a foaming tissue sealant for treating wounded tissue in a subject. The sealant can be formulated to include a compound or composition of the invention. The sealant is useful for significantly diminishing or preventing blood or fluid loss from injured tissues, organs or blood vessels, while also providing a barrier to infection.

Another quorum sensing activity is biofilm formation. Biofilms are communities of bacterial cells adhered to surfaces. Biofilms are highly problematic in industrial processes such as clogging of cooling towers in manufacturing plants. The novel strategies of the present invention prevent or disrupt biofilms by interfering with quorum sensing.

In another embodiment, the invention provides a method of removing a biofilm from a surface that comprises treating the surface with a compound of the invention. The surface is preferably the inside of an aqueous liquid distribution system, such as a drinking water distribution system or a supply line connected to a dental air-water system, where removal of biofilms can be particularly difficult to achieve. The compound is preferably applied to the surface either alone or together with other materials such as conventional detergents or surfactants.

A further embodiment of the invention is an antibacterial composition comprising a small molecule compound of the invention together with a bacteriocidal agent. In the antibacterial compositions, the compound of the invention helps to remove the biofilm while the bacteriocidal agent kills the bacteria. The antibacterial composition is preferably in the form of a solution or suspension for spraying and/or wiping on a surface.

In yet another aspect, the invention provides an article coated and/or impregnated with a compound of the invention in order to inhibit and/or prevent biofilm formation thereon. The article is preferably composed of plastic with the compound of the invention distributed throughout the material.

It is further envisioned that the small molecule compounds or compositions of the invention can be used to inhibit bacterial cell growth and biofilm formation in or on products or devices used for personal hygiene. Soap, toothpaste, dental floss, laundry detergent or moisturizing lotion are examples of consumer products that would benefit from the inclusion of the small molecule compounds or composition of the invention. In addition, such a compound or composition can be included in a personal hygiene device such as a toothbrush, tongue depressor, or any other such device which comes in contact with a tissue.

Thus, the invention includes introduction of one or more small molecules of the invention into an environment where it is desired to prevent bacteria from acting communally in an undesirable activity such as in production of biofilms or virulence. Introduction of the small molecules of this invention is also contemplated as treatment where undesirable bacterial communities are already established. The particular quantity of the small molecule for prevention or treatment is to be determined experimentally by methods known to those skilled in the art. An example provided herein for guidance involves prevention of virulent bacterial activity in the animal model Caenorhabditis elegans.

Quorum sensing, a process of bacterial cell-cell communication, relies on production, detection, and response to autoinducer signaling molecules. LuxN, a nine transmembrane domain protein from Vibrio harveyi, is the founding example of membrane-bound receptors for acyl-homoserine lactone (AHL) autoinducers. Previously, nothing was known about signal recognition by membrane-bound AHL receptors. Using mutagenesis and suppressor analyses, the AHL-binding domain of LuxN has now been characterized. To extract signaling parameters, a strong LuxN antagonist was exploited, one of the fifteen small-molecule antagonists that were identified. Also identified as antagonists were phenoxyacetamides, e.g., N-cyclopentyl-2-(4-(2-phenylpropan-2-yl)phenoxy) acetamide and N-sec-butyl-2-(4-(2-phenylpropan-2-yl)phenoxy) acetamide.

From membrane-topology analysis, it would appear that LuxN is bound to the bacterial inner-membrane by nine trans-membrane (TM) spanning helices (FIG. 1B). From reporter-protein fusion analyses, it would appear that the N-terminus of LuxN is on the periplasmic side of the bacterial inner-membrane, while the histidine-kinase portion of LuxN resides in the cytosol (Jung et al., 2007). Therefore, LuxN contains four periplasmic loops and four cytosolic loops connecting the nine transmembrane domain (TM) segments (FIG. 1B). By analogy to homologous membrane-bound sensor kinases, LuxN is believed to assemble into homodimers.

To locate the AI-1 binding domain of LuxN, a genetic screen was performed to identify luxN mutants encoding proteins incapable of properly responding to AI-1 (Example 1). All of the identified amino-acid mutations that affect AI-1 signaling cluster in TM helices near the periplasmic face, or are located within periplasmic loops, indicating that LuxN most likely binds AI-1 on the periplasmic side of the membrane (FIG. 1B). The results indicated that the LuxN AI-1 binding domain is composed of TM helices 4, 5, 6, and 7 as well as the intervening periplasmic loops 2 and 3.

The large number of mutations identified in this work that affect AI-1 binding suggest that LuxN makes multiple contacts with AI-1. Further supporting our conclusion that TM4, TM5, TM6, and TM7 and periplasmic loops 2 and 3 encode the AI-1 binding domain of wild-type LuxN, a LuxN homolog was recently discovered that lacks the first 80 amino acids, which encode TM1, TM2, and periplasmic loop 1, indicating that this region of LuxN is dispensable for AI-1 binding and signaling (FIG. 2 and NCBI database). This truncated LuxN homolog retains all of the critical regions identified in our identified AI-1 binding domain, indicating that this LuxN variant can still respond to an autoinducer molecule (FIG. 2). Interestingly, the most highly conserved domain in LuxN is centered at position P226, and contains a PPAL motif that is 100% conserved among all known LuxN homologs (FIG. 2). Both proline residues of this motif were identified as critical for LuxN signaling by our random mutagenesis screen. Therefore, we deduce that the PPAL motif is essential for LuxN signal transduction.

Sequence alignment comparison of V. harveyi LuxN with other LuxN homologs confirmed that the homologs have conserved binding pockets that accommodate an AHL-type ligand and that likewise accommodate the small molecule compounds of this invention (FIG. 2). These small molecules antagonize a broad spectrum of AHL type receptors.

A high-throughput chemical screen was used to identify the set of small molecules that were specifically demonstrated to antagonize the LuxN/AI-1 interaction in the model system of V. harveyi (Example 4). All of these LuxN antagonist molecules have IC₅₀ values in the low micromolar range, and, based on competition assays and genetic evidence, the most potent LuxN antagonist competes for the AI-1 binding site. These antagonists provided a molecular tool with which to further probe the AI-1 binding pocket and characterize the signaling properties of V. harveyi LuxN.

These are the first antagonist molecules that target an AHL membrane-bound sensor kinase. Importantly, the antagonists identified by this screen are not similar in structure to AI-1 (see, for example, FIG. 4A). Therefore, it is unlikely that rational-design experiments would have predicted these molecules as AHL antagonists. To explore whether the antagonists competed with AI-1 for binding to LuxN, we performed an antagonist-suppressor screen, and identified LuxN* I209F, which is not antagonized by C450-0730 (Example 6). Importantly, this mutation lies on the periplasmic side of TM 6, in the center of the proposed AI-1 binding domain, consistent with the possibility that C450-0730 competes for the AI-1 binding site (though the LuxN* mutation I209F does not affect AI-1 signaling). The AI-1 dose-response curves in the presence of different concentrations of C450-0730 for both wild-type LuxN and LuxN F163A provided a good data collapse indicative of competitive inhibition (FIGS. 4B and 4C). Combined, these results led to the conclusion that the C450-0730 antagonist is competing for the AI-1 binding pocket of LuxN. Because the LuxN* I209F mutation only affects the antagonistic ability of C450-0730, but does not interfere with AI-1 signaling, we deduce that C450-0730 makes at least some contacts with LuxN that are distinct from those made by AI-1.

In order to answer the question whether mutations in LuxN could shift the free-energy bias between receptor kinase and phosphatase states, a model was devised, shown schematically in FIG. 14. We propose that each LuxN can exist in any of four states: kinase (on) or phosphatase (off), with ligand bound or unbound. Receptor activity is determined by the thermal equilibrium among these states, characterized by the free-energy difference f between the on and off states of LuxN (see Experimental Procedures). Within the model, the measured output, bioluminescence, is the same unknown function of f for all strains, reflecting the fact that bioluminescence depends only on receptor activity, which at equilibrium depends only on f. The model predicts that mutations can cause EC₅₀ to increase or decrease depending on the sign of the shift in Δε the free-energy bias between kinase and phosphatase states. Indeed, the model is nicely supported by the data collapse in FIG. 4C, where the bioluminescence for the LuxN F163A mutant collapses well with wild type assuming only a shift in Δε. More generally, we have found that the bioluminescence data for many of our LuxN mutants collapse well with the combined wild-type and LuxN F163A data, allowing us to deduce changed Δε values and in some cases also changed binding affinities (FIG. 15). This analysis supports a close functional analogy between LuxN and E. coli chemotaxis receptors, and suggests the general relevance of two-state, free-energy models for bacterial sensor kinases.

Little was known about how membrane-bound kinase proteins, like LuxN, detect AHLs. Our mutagenesis strategy, showing that LuxN most likely binds AI-1 on the periplasmic side of the membrane, indicates that AI-1 is released from V. harveyi, accumulates in the extracellular space, and subsequently triggers the LuxN quorum-sensing cascade. This mechanism is distinct from the previously characterized LuxR-type AHL-signaling mechanism. Typically, LuxR-type AHL receptors require significant intracellular AHL concentrations for folding. Thus, at low cell densities the LuxR proteins do not fold properly and are degraded, so quorum sensing does not occur. Degradation of the LuxR-type proteins in the absence of the AHL signal is presumed to be a mechanism preventing premature activation of quorum sensing in canonical LuxR-AHL systems. Apparently, V. harveyi has evolved a distinct mechanism to circumvent short circuiting its quorum-sensing pathway, namely by compartmentalizing the cytosolic production of AI-1 in a location inaccessible to the periplasmic sensing domain of LuxN. This spatial uncoupling of AI-1 production from AI-1 binding allows V. harveyi to exclusively monitor extracellular levels of AI-1. It must be noted that V. harveyi has three quorum-sensing circuits, all of which have similar architectures. Thus, all three systems have signal production spatially uncoupled from signal detection (FIG. 1A).

Furthermore, through quantitative analysis it was revealed that, unlike the paradigmatic two-state chemotaxis receptors which spend roughly equal time in the active and inactive states for maximum sensitivity to ligand, the quorum-sensing receptor LuxN spends ˜96% of its time in the active/kinase state and requires establishment of a threshold concentration of autoinducer to inactivate it. Remarkably, although the chemotaxis and LuxN receptors are homologous, they solve fundamentally different biological problems by operating in different regimes. Chemotaxis, a system tuned for sensitivity, allows instantaneous alterations in behavior in response to small fluctuations in signal concentration. Quorum sensing, by contrast, a system built to ignore small perturbations, initiates a slow, all-or-nothing commitment program only upon reaching a signal threshold. We suggest that the distinct design properties inherent in the quorum sensing and chemotaxis signaling systems have evolved to optimally solve very different biological problems.

The following examples set forth the general procedures involved in practicing the present invention. To the extent that specific materials are mentioned, it is merely for purposes of illustration and is not intended to limit the invention. Unless otherwise specified, general molecular biology procedures, such as those set forth in Sambrook et al., Molecular Cloning, Cold Spring Harbor Laboratory (1989) (hereinafter “Sambrook et al.”) or Ausubel et al. (eds) Current Protocols in Molecular Biology, John Wiley & Sons (1998) (hereinafter “Ausubel et al.”) were used.

Example 1 Identification of LuxN Mutants with Defective Responses to AI-1

The aim of this study was to determine how LuxN and AI-1 interact in order to understand how trans-membrane receptors couple AHL signaling to changes in gene expression. However, as is the case for most histidine sensor kinases, the complex trans-membrane topology of LuxN makes direct structural analysis extremely difficult. Therefore, to pinpoint the AI-1 binding site in the periplasmic domain of LuxN, directed mutagenesis of the 1 kb region of luxN encoding the membrane-binding domain was performed using error-prone PCR. The library of luxN mutants generated by this approach was cloned into a version of the luxN gene lacking this region to regenerate full-length luxN. The mutant library was introduced into the double sensor mutant JMH625 (luxN luxQ), which has a bright phenotype because there is no flow of phosphate to LuxO (FIG. 1A). The CAI-1-CqsS system is intact in the strain used for this screen. Because saturating levels of CAI-1 are always present in these experiments, CqsS exists as a phosphatase and thus does not contribute in funneling phosphate to LuxO. Thus it is reasonable that when a wild-type copy of luxN is introduced into this strain in the presence of AI-1, it will remain bright because binding of AI-1 to LuxN induces phosphatase activity. However, if a mutant luxN allele encoding a LuxN protein that is incapable of binding or responding to AI-1 is introduced, it will confer a dark phenotype due to high levels of LuxN auto-phosphorylation and phospho-transfer to LuxO (FIG. 1A).

Approximately 30,000 luxN mutants were screened for those alleles causing a reduction in bioluminescence. Ten alleles were confirmed to produce dark phenotypes. These luxN genes were sequenced to identify the mutations (Table 2, FIG. 1B). Several candidates contained multiple mutations, and these mutations were uncoupled by site-directed mutagenesis to produce genes encoding LuxN proteins with single amino-acid substitutions (Table 2). Interestingly, in the case of LRS6 two of the uncoupled mutations independently caused dark phenotypes (Table 2). Further analyses were carried out on LuxN mutants containing only single amino-acid changes.

The mutations conferring dark phenotypes cluster to the periplasmic region of TMs 4, 5, 6, and 7 and periplasmic loops 2 and 3 (FIG. 1B circles) suggesting that the AI-1 binding site resides there. To explore this hypothesis further, the 11 available LuxN homologs were compared and every 100% conserved amino acid was replaced as well as the other most highly conserved amino acids within this region with alanine, and were screened as above. This analysis produced an additional 20 mutants defective in response to AI-1. (Table 1, FIG. 1B).

The LRS5 mutation, which confers a dark phenotype, is a single base-pair deletion at position 634 causing a premature stop codon at amino-acid residue 213 (Table 2). This mutation was unexpected because the premature stop codon would lead one to believe that the kinase domain of LuxN should not be synthesized, making it unclear how this mutation could confer a dark phenotype. To investigate this, a FLAG-epitope tag was fused to the C-terminus of this mutant LuxN and the protein was probed by western blot analysis. This analysis indicated that a truncated version of LuxN lacking approximately the first 220 amino acids is synthesized (data not shown). It appears that an alternative ribosome binding site exists downstream of the LRS5 deletion, enabling translation of a truncated form of LuxN. Because this truncation eliminates almost the entire proposed AI-1 binding domain from LuxN, only the cytoplasmic kinase domain is produced which, because it is unable to bind to AI-1, constitutively acts as a kinase causing a dark phenotype.

Example 2 LuxN Mutant Phenotypes

To characterize the signaling capabilities of the single-amino-acid-substituted LuxN mutants, a series of quantitative phenotypic analyses were carried out. First, we measured bioluminescence in stationary-phase cultures of strains carrying either wild-type luxN or each luxN allele conferring a dark phenotype. The bioluminescence produced by the strain with wild-type luxN was set at 100% (FIG. 6A). As negative controls, two luxN mutants harboring wild-type phenotypes (LuxN L138A and LuxN E154Q) which were randomly isolated from the screen were also included in the analysis and they produced the wild-type level of bioluminescence (FIG. 6A). By contrast, the LuxN mutants F151A, I153F, F155I, L166R, T214I, F220A, P226T, and S232N exhibited at least an 80% reduction in bioluminescence relative to wild type (FIG. 6A). To confirm that the dark phenotypes did not stem from increased LuxN protein levels, FLAG-epitope tags were incorporated at the C-terminus of a representative subset of the LuxN mutants shown in FIG. 6A as well as wild-type LuxN. Western blot showed that there were no differences in protein production (data not shown).

We reasoned that the LuxN mutants conferring dark phenotypes must be acting as kinases at high cell density, resulting in continued flow of phosphate through the quorum-sensing circuit. This in turn, should manifest itself in elevated qrr expression at high cell density (FIG. 1A). To test this idea, quantitative real-time PCR was performed and Qrr4 transcript levels were measured in each of the luxN mutant strains described above. As controls, Qrr4 transcript levels were measured in the wild type and the bright control strains, LuxN L138A and LuxN E154Q, and we found that indeed, in these three strains, Qrr4 levels are low, consistent with these LuxN proteins acting as phosphatases at high cell density (FIG. 6B). However, the luxN mutants exhibiting dark phenotypes (FIG. 6A) all have significantly increased Qrr4 transcript levels (10 to 30-fold higher than wild type) (FIG. 6B). This result confirms that the decrease in bioluminescence observed in the dark LuxN mutants is the direct result of an alteration in signaling through the LuxN quorum-sensing pathway.

Example 3 AI-1 Dose-Response Curves

Two possible mechanisms were considered underlying the dark LuxN phenotypes. First, a particular mutation could abolish AI-1 binding. If so, this type of mutation would cause LuxN to act as a kinase at high cell density in the presence of AI-1. Alternatively, a mutation could allow AI-1 binding, but disrupt the ability of LuxN to transduce the signal to the cytoplasm. We first determined which LuxN mutant proteins could bind AI-1 by measuring the AI-1 dose-response of each LuxN missense mutant. For this, V. harveyi strain HLS253 ΔluxMN, ΔluxPQ, ΔluxS was used. V. harveyi HLS253 is constitutively bright because the luxN and luxPQ genes, encoding the quorum-sensing receptors, have been deleted. Also, V. harveyi HLS253 does not produce AI-1 or AI-2, due to the luxM and luxS deletions, respectively. Introduction of a wild-type copy of luxN into V. harveyi HLS253 confers a dark phenotype because, in the absence of AI-1, LuxN acts as a constitutive kinase. However, addition of exogenous AI-1 to HLS253 harboring a wild-type copy of luxN induces bioluminescence. Introduction of a luxN mutant encoding a LuxN protein incapable of binding AI-1 or incapable of signaling the AI-1 binding event to the cytoplasm will confer a dark phenotype to HLS253. And, such defects will cause the LuxN proteins to remain as kinases even in the presence of AI-1. By contrast, if a particular LuxN mutant is introduced that is capable of binding AI-1, even with lower affinity than wild-type LuxN, these LuxN proteins will switch to phosphatase activity following the addition of sufficient AI-1, and bioluminescence will be induced.

To determine AI-1 EC₅₀ values, wild-type LuxN and each LuxN mutant were assayed for response to AI-1 at concentrations ranging from 24 pM to 500 μM. A subset of the dose-response curves is shown in FIG. 7A, and the remainder of the EC₅₀ data is provided in Table 1. The EC₅₀ for wild-type LuxN binding to AI-1 is 23 nM. The control mutants, LuxN L138A and LuxN E154Q, as expected, have EC₅₀ values of 30 nM and 55 nM, respectively, similar to wild-type LuxN (Table 1). Many of the LuxN mutants have drastically increased EC₅₀ values (Table 1). For example, LuxN I153F, F155A, F162A, T206A, and S232A have EC₅₀ values of 130 nM, 580 nM, 93 μM, 310 nM, and 400 nM, respectively (FIG. 7A). In five cases, LuxN L166R, F202A, S205P, P226T, and E233A, the mutants conferred a dark phenotype to V. harveyi even at 500 μM AI-1 (FIG. 7B) and therefore EC₅₀ values were unable to be assigned. Nonetheless, we successfully determined the AI-1 EC₅₀ values for 25 of the 30 LuxN mutants that conferred a dark phenotype. We conclude that LuxN mutant proteins that produce measurable EC₅₀ values, albeit higher than wild type, can bind AI-1 at least with some capacity.

Example 4 Identification of LuxN Antagonists

To probe the LuxN/AI-1 interaction further, small molecules were identified that interfere with V. harveyi quorum sensing by disrupting the binding of AI-1 to LuxN. To do this, a high-throughput chemical screen was carried out using the chemicals collection of the Broad Institute (Massachusetts, USA), which identified small molecules that specifically antagonize LuxN signaling in V. harveyi. The V. harveyi strain, JMH624 ΔluxPQ, ΔluxM, which lacks the AI-2 receptor, LuxPQ, as well as the AI-1 synthase, LuxM, was used for the antagonist screen. V. harveyi JMH624 is dark because there is no AI-2 receptor and the lack of AI-1 causes LuxN to act as a kinase (FIG. 1A). However, following exogenous addition of 20 nM AI-1, bioluminescence is induced because LuxN switches to phosphatase mode. Potential antagonist molecules were tested for the ability to reduce bioluminescence of V. harveyi JMH624 in the presence of 20 nM AI-1. To eliminate molecules causing general toxicity and those that interfere with luciferase or other downstream components of the quorum-sensing bioluminescence pathway, a second screen was carried out using a V. harveyi ΔluxN, ΔluxS control strain, JMH610. V. harveyi JMH610 lacks the AI-1 receptor LuxN and the AI-2 synthase, LuxS. In this case, because of the lack of AI-2, LuxQ acts as a kinase, and V. harveyi JMH610 is dark. However, following exogenous addition of AI-2, bioluminescence is induced because LuxQ switches to phosphatase mode (FIG. 1A). Any molecule that reduced bioluminescence in both JMH610 in the presence of AI-2 and JMH624 in the presence of AI-1 was eliminated from further analysis. Approximately 35,000 low-molecular-weight compounds were screened for specific inhibition of bioluminescence through the LuxN quorum-sensing pathway; 45 molecules were selected for further analysis, and a representative subset of these molecules with varying levels of antagonistic activity is shown in FIG. 4A. For example, molecule C450-0730 has an IC₅₀ value of 2.7 μM while a weaker antagonist, 3578-0898 has an IC₅₀ of 62.3 μM. Interestingly, the molecular cores of two of the strongest LuxN antagonists, C450-0730 and C646-0078, are very similar (FIG. 4A). A larger subset of these molecules is shown in FIG. 8.

It was not initially known whether the potent LuxN antagonist, C450-0730, was competing for the LuxN AI-1 binding site. To examine this, AI-1 EC₅₀ values were determined in the presence of 0 μM, 1 μM, and 10 μM C450-0730. Our rational is that, if C450-0730 competes with AI-1 for binding, the AI-1 EC₅₀ value should increase with increasing concentrations of C450-0730. Indeed, this is the case, as the AI-1 EC₅₀ values are 23 nM, 76 nM, and 376 nM at 0 μM, 1 and 10 μM C450-0730, respectively (FIG. 4B). Indeed, the AI-1 dose-response curves at these three C450-0730 concentrations can be collapsed onto a single curve, consistent with competitive inhibition (FIG. 4C and Experimental Procedures). The principal underlying the data collapse is that there is a fixed (albeit initially unknown) quantitative relation between measured bioluminescence and the free-energy difference between the active and inactive configurations of LuxN (Keymer et al., 2006). Therefore, all the dose-response curves should reproduce this same relation, i.e. the curves should “collapse” when bioluminescence is plotted versus free-energy difference. However, to plot the data this way, it is necessary to know how to relate ligand concentrations to free-energy differences, which means that it is necessary to know the ligand dissociation constants K_(D) for both the active and inactive configurations of LuxN. In practice, we iteratively improve our estimates for K_(D) values by attempting to collapse the dose-response curves and infer the true values from the best data collapse. This is a reliable procedure here, since the dose-response curves contain more data than the number of unknown K_(D) values. A major benefit of collapsing the data in this way is that it allows us to deduce the state-dependent K_(D) values for LuxN from the in vivo data: in the phosphatase (off) state K_(off) ^(AI-1)≈1 nM, and in the kinase (on) state K_(on) ^(C450-0730)≈500 nM.

We had reasoned that the dark phenotypes of our LuxN mutants could stem from (i) a defect in the ability to bind AI-1, (ii) a bias favoring the kinase state, (iii) a defect in signaling, or (iv) some combination of the above. The method of data collapse provides a powerful tool to distinguish among these possibilities. For example, consider the case of the mutant LuxN F163A (FIG. 4B) which has an AI-1 EC₅₀ value 378-fold higher than that of wild-type LuxN and for which dose-response curves were obtained in the presence of 0 μM, 1 and 10 μM of the antagonist C450-0730. First, we were able to collapse the three antagonist dose-response curves using the identical K_(on/off) ^(AI-1/C450-0730) as we used to collapse the wild-type LuxN data, indicating that LuxN F163A is not defective in its ability to bind AI-1 (eliminating possibility (i)). Second, the LuxN F163A data could all be collapsed onto the wild-type LuxN antagonist curves simply by adjusting the free-energy bias between the kinase (on) and phosphatase (off) states (FIG. 4C). This analysis allows us to conclude that LuxN F163A has an increased AI-1 EC₅₀ value exclusively because it has an altered free-energy bias that favors the kinase (on) state, establishing that possibility (ii) accounts for the dark phenotype of this mutant. Similar analysis applied to our other dark mutants reveals examples of the different possibilities and allows us to deduce and quantify the origins of the dark phenotypes.

Example 5 Antagonist Suppressor Analysis

To better understand the mechanism of C450-0730 interaction with LuxN, a suppressor screen was performed to identify LuxN mutants no longer antagonized by C450-0730. Using error-prone PCR, 2,000 mutants in the luxN N-terminal region were generated and conjugated into the V. harveyi ΔluxMN ΔluxPQ ΔluxS strain, HLS253, and arrayed in 96-well micro-titer plates. As mentioned, V. harveyi HLS253 is constitutively bright due to the absence of the quorum-sensing receptors, LuxN and LuxPQ, and both autoinducer synthases, LuxM and LuxS. To verify our strategy, a wild-type luxN control plasmid was also conjugated into V. harveyi HLS253, which conferred a dark phenotype because wild-type LuxN is a kinase in the absence of AI-1. Bioluminescence is restored to HLS253 containing wild-type luxN by the exogenous addition of 100 nM AI-1. We found that 800 nM C450-0730 was required to inhibit bioluminescence of HLS253 carrying wild-type luxN in the presence of 100 nM AI-1. The luxN mutant library was screened in the presence of 100 nM AI-1 and 800 nM C450-0730 for luxN alleles that enabled bioluminescence in V. harveyi HLS253. To eliminate luxN null mutants, the luxN mutant library was also screened in V. harveyi HLS253 in the absence of both AI-1 and C450-0730. The luxN alleles that conferred a bright phenotype in the absence of AI-1 were not examined further. Five LuxN mutant strains, LRS112, LRS311, LRS129, LRS147, and LRS1511 (Table 2) displayed dark phenotypes in the absence of AI-1 and C450-0730, but were bright in the simultaneous presence of AI-1 and C450-0730, suggesting that these LuxN proteins were no longer antagonized by C450-0730. The luxN mutations were sequenced to identify the alleles (Table 2). Interestingly, LuxN G271D was identified twice. From here forward this class of suppressor mutants is referred to as LuxN*.

Example 6 Characterization of the LuxN* Mutants

We speculated that the LuxN* mutants could have increased AI-1 sensitivity or decreased C450-0730 binding ability. To distinguish between these two possibilities, the LuxN* AI-1 EC₅₀ values were determined (FIG. 9A). As a reference, the dark mutant LuxN F163A is also included in FIG. 9A. The EC₅₀ value of wild-type LuxN is 23 nM, while LuxN* S184N is 11 nM, LuxN* I209F is 39 nM, LuxN* R245L is 4.8 nM, and LuxN* G271D is 3.7 nM (Table 1). Interestingly, three of the four LuxN* mutants, LuxN S184N, R245L, and G271D show increased sensitivity to AI-1, suggesting that these alleles circumvent C450-0730 antagonism through increased AI-1 binding or signaling or via a bias to the phosphatase state of LuxN (see Discussion). However, LuxN* I209F responded more like wild type to AI-1 as indicated by an AI-1 EC₅₀ value of 39 nM (Table 1).

In the reciprocal experiment, we determined the ability of C450-0730 to antagonize the LuxN* mutants. C450-0730 IC₅₀ values were measured by titrating C450-0730 from 0.64 nM to 50 μM, while keeping the AI-1 concentration constant at 10 nM. The C450-0730 concentration required to inhibit LuxN* G271D, R245L, and S184N was similar to that required to inhibit wild-type LuxN, indicating that the observed “resistance” to C450-0730 was indeed due to increased sensitivity to AI-1. However, a 5-fold higher concentration of C450-0730 was required to antagonize LuxN* I209F. Therefore, the LuxN* I209F mutation appears to affect C450-0730 binding. Because I209 is located within our proposed AI-1 binding site (FIG. 1B in triangle), and because it also affects C450-0730 antagonistic activity, we propose that C450-0730 could compete for the AI-1 binding site of LuxN. This conclusion is strongly supported by the good data collapse in FIG. 4C, which is based on competitive inhibition by C450-0730.

Example 7 Sensitive LuxN* Mutations are Epistatic to the LuxN Dark Mutations

For chemotaxis receptors in E. coli, adaptive methylation of specific cytoplasmic residues is known to additively bias receptors toward a kinase-active state. By analogy, we wondered whether some of our single-residue mutations might bias LuxN toward kinase or phosphatase states in an additive manner. To determine whether the LuxN G271D, R245L, and S184N mutants which have lower than wild type AI-1 EC₅₀ values are biased toward the phosphatase state, these mutations were engineered into the LuxN F163A mutant to test if they could shift the high EC₅₀ of LuxN F163A back toward a low EC₅₀. As a reminder, the F163A LuxN mutation has an increased AI-1 EC₅₀ value of 8.7 μM as compared to 23 nM for wild-type LuxN; therefore, it requires approximately 378 times more AI-1 to switch LuxN F163A into the phosphatase mode than the amount of AI-1 required to switch wild-type LuxN. A double mutant (LuxN F163A/R245L), a triple mutant (LuxN F163A/R245L/S184N), and a quadruple mutant (LuxN F163A/R245L/S184N/G271D) of LuxN were tested for their ability to respond to AI-1 (FIG. 9B). The incorporation of each LuxN* mutation into the context of the F163A mutation successively decreased the AI-1 EC₅₀ value approximately 10-fold, while the quadruple mutant had a constitutively bright phenotype (Table 1). From this analysis, we inferred that the LuxN* mutations are additive in their ability to bias LuxN toward the phosphatase mode.

Example 8 LuxN Antagonists Also Antagonize Cytoplasmic LuxR-Type Homoserine Lactone Receptor

LuxN is the founding member of an increasingly large family of membrane bound homoserine lactone autoinducer binding proteins. In this receptor family, autoinducer binding information is transduced to a DNA binding protein by phosphorylation. There are two quorum sensing mechanisms for homoserine lactone autoinducer detection. First, through membrane bound receptors homologous to V. harveyi's LuxN (FIG. 10A). Second, by cytoplasmic LuxR-type proteins, such as CviR from Chromobacterium violaceum, in which binding of the homoserine lactone signal allows the LuxR-type receptor protein to fold and bind DNA to alter transcription (FIG. 10B).

After having successfully screened for antagonists of LuxN, the membrane bound homoserine lactone receptor, we tested whether these same antagonists could antagonize a cytoplasmic LuxR-type homoserine lactone receptor. We used Chromobacterium violaceum CviR because inhibition results in loss of purple pigment production (FIG. 11). Five of the LuxN antagonists greatly inhibited the cytoplasmic CviR receptor. These data show that these molecules work on both the outside and the inside of the bacterial cell.

Molecule 4606-4237 allows the CviR protein to fold and bind DNA exactly as does the endogenous homoserine lactone ligand. However, the CviR-4606-4237 complex cannot activate transcription.

Example 9 Antagonist Molecules Inhibit Pathogenicity in Bacterial Pathogenesis Model System

Chromobacterium violaceum is pathogenic to the nematode Caenorhabditis elegans. This is a classic bacterial-host pathogenesis model. Killing of C. elegans is quorum-sensing controlled. As such, ΔCviI (homoserine lactone production) and ΔCviR (cytoplasmic receptor) mutants of C. violaceum are avirulent (FIG. 5). Wild type C. violaceum were pathogenic in C. elegans with median survival time of two days. In contrast, C. elegans infected with mutant C. violaceum that lacked a functioning CviI gene (controlling homoserine lactone production) or CviR gene (autoinducer receptor protein) had a median survival time of ten days or eleven days, respectively. Molecule 4606-4237, a thiolactone, inhibits C. violaceum from killing the nematodes (FIG. 13). This example utilized the synthase mutant strain (CviI) of C. violaceum (median survival 12 days) to infect C. elegans. When the bacteria were supplemented with exogenous homoserine lactone (HSL) autoinducer, the median survival of C. elegans was reduced to 4 days. However, the effect of HSL was abolished when the bacteria were supplemented with a combination of homoserine lactone and the thiolactone antagonist 4606-4237. Under those conditions, the median survival of C. elegans was 12 days. When the bacteria were supplemented with the thiolactone antagonist alone, median survival was 14 days. Inhibition requires CviR (the cytoplasmic receptor protein).

Experimental Procedures of the Examples

Bacterial Strains and Media

All V. harveyi strains were derived from V. harveyi BB120 and grown aerobically at 30° C. in either Luria-Marine (LM) broth or Autoinducer Bioassay (AB) broth. Plasmids were maintained in E. coli strain XL10Gold (Stratagene) at 37° C. in LB broth. Tri-parental conjugations were performed with the helper plasmid pRK2013 as described (Ditta, G., et al. (1980). Proc Natl Acad Sci USA 77, 7347-7351). When needed, chloramphenicol (Cm) was added to a final concentration of 10 μg/ml and IPTG to a final concentration of 500 μM. A list of strains and plasmids used in this study is provided in Table 3.

DNA Manipulations

DNA manipulations were performed as described in Sambrook et al (Sambrook et al., 1989). PCR reactions were performed using Herculase Enhanced DNA polymerase (Stratagene). Restriction endonucleases, dNTPs, and T4 ligase were purchased from New England Biolabs. Site-directed mutagenesis was performed using the Quickchange II Site-Directed mutagenesis kit (Stratagene). QIAGEN methods were used for plasmid preparations and PCR cleanups. Sequences of primers are available by request.

LuxN Mutant Library Construction

The luxN gene was amplified from wild-type V. harveyi BB120 by PCR and cloned into vector pFED343 at the EcoRI and NcoI sites, making pLS1001. Mutagenesis of the first 950 bases of luxN was performed using the error-prone PCR kit Genemorph II EZclone (Stratagene). Resulting mutations were cloned into vector pFED343. The luxN mutant library was conjugated into V. harveyi ΔluxN ΔluxPQ strain, JMH625. Ex-conjugates were selected on LM medium agar supplemented with Cm. Approximately 30,000 mutants were screened for reduced bioluminescence. Plasmids from dark mutants were isolated and backcrossed into V. harveyi JMH625 to confirm phenotypes. The luxN genes were sequenced and all mutations were engineered independently using Quikchange site-directed mutagenesis (Stratagene). All single luxN mutant constructs were conjugated into V. harveyi JMH625 to verify the phenotypes.

V. harveyi Strain Construction

To construct the V. harveyi ΔluxMN, ΔluxPQ, ΔluxS mutant strain, HLS253, the luxMN operon was deleted from strain FED119 (Neiditch, M. B., et al. (2006). Cell 126, 1095-1108). Specifically, cosmid pBB1754, carrying luxMN was modified by deleting DNA specifying the entire luxMN open reading frame. The resulting plasmid, p1754:: ΔluxMN, was introduced into V. harveyi FED119, and the deletion transferred to the chromosome to generate V. harveyi strain, HLS253.

Bioluminescence Assays

AI-1 dose-response curves were generated in V. harveyi strain HLS253 containing a vector with wild-type luxN or one of the luxN mutants. V. harveyi strains were grown overnight in LM medium containing Cm and diluted 1:10000 in AB medium plus Cm and 0.5 mM IPTG in triplicate in 96-well microtiter plates. AI-1 was added at either 100 μM or 500 μM and serial 4-fold dilutions were made to final AI-1 concentrations of 24 pM and 119 pM, respectively. The cultures were allowed to grow to stationary phase, at which time bioluminescence and optical density were measured using a Perkin Elmer Envision plate reader.

Quantitative Real-Time PCR Analysis

Wild type and luxN mutant V. harveyi strains were grown in LM medium in triplicate to an OD₆₀₀ of 1.0 after which cell pellets were isolated and flash-frozen using liquid nitrogen. Pellets were stored at −80° C. prior to RNA isolation. RNA was isolated and treated with DNase using the Ribo-Pure-Bacteria kit (Applied Biosystems; Foster City, Calif.). RNA was quantified and 1 μg of RNA was converted to cDNA using Superscript H reverse transcriptase (Invitrogen; Carlsbad, Calif.). Quantitative real-time PCR analysis was performed with primers for qrr4 and hfq, where hfq served as an internal control (Tu and Bassler, 2007).

Screen for LuxN Antagonists

The V. harveyi strains, JMH624 and JMH610 were grown overnight in AB medium and diluted 1:100 prior to the exogenous addition of either 20 nM AI-1 or 20 nM AI-2, respectively. The diluted cultures were dispensed into 384 well micro-titer plates and the potential antagonist molecules were added to each well. Each micro-titer plate was duplicated to eliminate variance. The 35,000 molecule library was supplied by the Broad Institute and the Initiative for Chemical Genetics (Cambridge, Mass.). Antagonist activity was measured as a function of bioluminescence on a PerkinElmer Envision plate reader.

LuxN Suppressor Screen

The luxN mutant library was conjugated into V. harveyi strain HLS253 and selected on LM containing Cm. Colonies were inoculated into 96-well micro-titer plates containing LM broth and Cm and grown at 30° C. with aeration to stationary phase. Glycerol was added to a final concentration of 20%, and the library was stored at −80° C. Frozen stocks were partially thawed and used to inoculate duplicate 96-well micro-titer plates containing AB medium with Cm and IPTG. To one plate, 100 nM AI-1 and 800 nM antagonist C450-0730 was added, while the duplicate control plate had neither AI-1 nor C450-0730 added. The plates were incubated at 30° C. with aeration until the cultures reached stationary phase, at which time bioluminescence was measured and the two plates compared. Strains from wells that produced light in the AI-1/C450-0730 plates but did not produce light in the control plates (no AI-1/no C450-0730) were analyzed further. The luxN mutant plasmids were sequenced to determine the mutations responsible for the observed phenotypes and the mutations were reengineered using Quikchange site-directed mutagenesis (Stratagene; La Jolla, Calif.).

LuxN Free Energies, Competitive Binding, and Data Collapse

In equilibrium, the probability for a LuxN to be active as a kinase is determined by the free-energy difference, f=f_(on)−f_(off), between its kinase (on) and phosphatase (off) states according to

$\begin{matrix} {p_{on} = {\frac{1}{1 + e^{f}}.}} & \left( {{Eq}.\mspace{14mu}{\# 1}} \right) \end{matrix}$ (We measure all energies in units of the thermal energy k_(B)T.) Assuming competitive binding of AI-1 and C450-0730, one obtains

$\begin{matrix} {{f = {{\Delta ɛ} + {\log\left( \frac{1 + \frac{\left\lbrack {{AI}\text{-}1} \right\rbrack}{K_{off}^{{AI}\text{-}1}}}{1 + \frac{\left\lbrack {{AI}\text{-}1} \right\rbrack}{K_{on}^{{AI}\text{-}1}}} \right)} + {\log\left( \frac{1 + \frac{\left\lbrack {C\; 450\text{-}0730} \right\rbrack}{K_{off}^{C\; 450\text{-}0730}}}{1 + \frac{\left\lbrack {C\; 450\text{-}0730} \right\rbrack}{K_{on}^{C\; 450\text{-}0730}}} \right)}}},} & \left( {{Eq}.\mspace{14mu}{\# 2}} \right) \end{matrix}$ where K_(on/off) ^(AI-1/C450-0730) is the dissociation constant for the given state and ligand, and the “bias” Δε is the value of f at zero ligand concentration (Keymer, J. E., et al. (2006). Proc Natl Acad Sci USA 103, 1786-1791).

To test for competitive binding of C450-0730 to LuxN, we assume that bioluminescence is some (unknown) function of the fraction of LuxN proteins that are active as kinases, i.e. bioluminescence is a function of f. We therefore plot bioluminescence as a function of f−Δε_(WT), as given in Eq. #2, and search for the values of K_(on/off) ^(AI-1/C450-0730) that collapse all of our data onto a single curve. The results are shown in FIG. 4C.

To quantitatively test whether LuxN mutations that shift AI-1 EC₅₀ values can be attributed to changes in the bias Δε and/or the AI-1 binding affinities, we attempted to collapse the AI-1 dose-response curves for each mutant onto the wild-type curve (FIG. 15B) using Δε_(mutant)−Δε_(WT) and in some cases K_(off) ^(AI-1) as fitting parameters. The collapse was satisfactory for many but not all cases, as discussed in the text.

TABLE 1 LuxN Mutant Phenotypes Fold Lux change in Allele Phenotpye AI-1 EC₅₀ (M) EC₅₀ ^(a) Location Wild type WT 2.3 × 10⁻⁸ H46Y WT NM TM2 S54P WT NM TM2 A77D WT NM PL1 H155Q WT NM CL1 N133A ^(b) Dark 8.2 × 10⁻⁸ 3.6 TM4 L138A WT 3.0 × 10⁻⁸ 1.3 TM4 T139A WT 1.4 × 10⁻⁸ 0.6 TM4 T139I Dark 7.4 × 10⁻⁸ 3.2 TM4 V140A WT NM PL2 V143A Dark 9.9 × 10⁻⁸ 4.3 PL2 I145A WT NM PL2 P148A WT NM PL2 S149A WT 6.1 × 10⁻⁸ 2.7 PL2 F151A Dark 6.9 × 10⁻⁵ 3000 PL2 I153A Dark 1.2 × 10⁻⁶ 52.2 PL2 I153F Dark 1.3 × 10⁻⁷ 5.7 PL2 I153L WT 6.6 × 10⁻⁸ 2.9 PL2 E154Q WT 5.5 × 10⁻⁸ 2.4 PL2 E154A WT NM PL2 F155A Dark 5.8 × 10⁻⁷ 25.2 PL2 F155I Dark 8.1 × 10⁻⁴ 35217 PL2 F155L Dark 4.1 × 10⁻⁶ 178.3 PL2 G156A WT NM PL2 P157A WT NM PL2 F162A Dark 9.3 × 10⁻⁵ 4043 TM5 F163A Dark 8.7 × 10⁻⁶ 378.3 TM5 L166A Dark NA TM5 L166R Dark 2.3 × 10⁻⁷ 10.0 TM5 V170A WT NM TM5 T173A WT NM TM5 N176A WT NM TM5 S184N Sensitive 1.1 × 10⁻⁸ 0.5 CL2 K186A WT NM CL2 L187A WT NM CL2 A190T WT NM CL2 K191A WT NM CL2 Y194A WT NM TM6 G198A WT NM TM6 I199A WT NM TM6 F202A Dark NA TM6 F202Y Dark 7.1 × 10⁻⁷ 30.9 TM6 S205A WT 3.2 × 10⁻⁸ 1.4 TM6 S205P Dark NA TM6 T206A Dark 3.1 × 10⁻⁷ 13.5 TM6 I209F WT 3.9 × 10⁻⁸ 1.7 TM6 G212A WT 3.6 × 10⁻⁸ 1.6 TM6 T214A Dark 4.5 × 10⁻⁷ 19.6 TM6 T214I Dark 7.0 × 10⁻⁵ 1043 TM6 D219A Dark 1.3 × 10⁻⁷ 5.7 PL3 F220A Dark 1.9 × 10⁻⁴ 8261 PL3 F220I Dark 7.1 × 10⁻⁴ 30870 PL3 S221A Dark 1.9 × 10⁻⁷ 8.3 PL3 W224A Dark 1.9 × 10⁻⁷ 8.3 TM7 L225A WT 5.5 × 10⁻⁸ 2.4 TM7 P226A Dark 2.3 × 10⁻⁴ 10000 TM7 P226T Dark NA TM7 P227A Dark 4.0 × 10⁻⁶ 173.9 TM7 P227L Dark 3.9 × 10⁻³ 169565 TM7 L229A WT NM TM7 S230A WT NM TM7 S232A Dark 4.0 × 10⁻⁷ 17.4 TM7 S232N WT 4.1 × 10⁻⁸ 1.8 TM7 E233A Dark NA TM7 M234I WT NM TM7 M234A WT NM TM7 G238A WT NM TM7 Y239A WT NM TM7 R245L Sensitive 4.8 × 10⁻⁹ 0.21 CL4 V249I WT NM CL4 G271D Sensitive 3.7 × 10⁻⁹ 0.16 TM8 F163A/ Dark 3.7 × 10⁻⁶ 160.9 R245L F163A/ Dark 1.4 × 10⁻⁷ 6 R245L/ S184N F163A/ Sensitive NA R245L/ S184N/ G271D ^(a)Fold change in EC₅₀ value with respect to wild-type EC₅₀ value. ^(b)Bold indicated 100% conserved amino acids. (See FIG. 2) TM (Trans-Membrane Domain) CL (Cytoplasmic Loop) PL (Periplasmic Loop) NM (Not Measured) NA (Not Applicable)

TABLE 2 LuxN Mutants Identified in the Random Mutant Screen. Strain Allele LRS3 P226T ^(a) LRS5 Basepair 634 deleted LRS6 F155L, A190T, F202Y LRS11 S205P LRS12 T214I LRS13 H46Y, F220I, V249I LRS14 G212A, T214I LRS16 S54P, H115Q, T139I LRS19 A77D, P227L, S232N, M234I LRS20 D219A LRS112 V21M, G165D, S184N LRS311 I209F LRS129 F93L, G271D, L292H LRS147 M217I, G271D LRS1511 R247L, Y301F ^(a)Bold indicates alleles that confer a defective LuxN phenotype when tested independently.

TABLE 3 Strains and Plasmids Used in this Study. Strain or Plasmid Relevant Feature Reference or Source BB120 Wild type (Bassler et al., 1997) JMH624 ΔluxM luxQ::Tn5 unpublished JMH625 ΔluxN luxQ::Tn5 (Henke and Bassler 2004b) JMH610 ΔluxS luxN::Tn5 (Neiditch et al., 2006) BB721 luxO::Tn5 (Bassler et al., 1994) FED119 ΔluxPQ ΔluxS luxN::Tn5 (Neiditch et al., 2006) HLS253 ΔluxMN ΔluxPQ ΔluxS This Study pRK2013 Broad host range, tra, Kan^(r) (Ditta et al., 1980) pPHIJ1 Broad host range, tra, mob, Gm^(r) (Beringer, 1978) pCP20 Ts FLP recombinase plasmid; Amp^(r) (Datsenko and Wanner 2000) pBB1754 pLAFR with luxMN::TN5 (Bassler et al., 1993) pLS1121 pBB1754 with ΔluxMN This Study pFED343 pEVS143 Cm^(r) Unpublished pLS1001 pFED343 with luxN locus This Study

All publications and patents mentioned in this document are herein incorporated by reference. The present invention is not limited to the embodiments described and exemplified above, but is capable of variation and modification within the scope of the appended claims. 

The invention claimed is:
 1. An isolated compound characterized by its ability to bind to Vibrio harveyi LuxN at the autoinducer-1 (AI-1) binding site of LuxN, wherein said compound is of the structures from the group consisting of:


2. A method of disrupting detection of acyl-homoserine lactone-type autoinducer in Gram-negative bacteria comprising contacting the bacteria with the compound of claim
 1. 3. A pharmaceutical composition comprising one or more compounds of claim 1 and a pharmaceutically acceptable carrier, excipient or diluent.
 4. A bacterial biofilm-inhibiting composition comprising one or more compounds of claim 1 and DMSO.
 5. A method of treating a bacterial infection of Gram-negative bacteria, comprising administering to a subject having a bacterial infection, a therapeutically effective amount of a compound of claim 1, wherein the bacteria is of a type that controls virulence factors by quorum sensing.
 6. A method of controlling growth of quorum sensing Gram-negative bacteria attached to a solid surface, comprising exposing the bacteria to a composition comprising one or more compounds of claim 1, in an amount that affects biofilm formation.
 7. A method of controlling virulence factor expression in Gram-negative bacteria comprising contacting the bacteria with a composition comprising one or more compounds of claim
 1. 8. A method of preventing biofilm formation comprising administering the compound of claim 1 to a surface.
 9. The method of claim 8 wherein the surface is a solid material.
 10. A method of inhibiting quorum sensing-mediated activity in Gram-negative bacteria comprising contacting the bacteria with the compound of claim
 1. 11. The method of claim 10 wherein the activity is pathogenicity.
 12. The method of claim 11 wherein the bacterial species is selected from the group consisting of V. harveyi and C. violaceum.
 13. The method of claim 11 wherein the bacterial species is Chromobacterium violaceum.
 14. The method of claim 11 wherein the bacteria are pathogenic to humans or animals.
 15. The method of claim 11 wherein the bacteria are pathogenic to plants.
 16. The method of claim 11 wherein the bacteria are pathogenic to marine life.
 17. The method of claim 10 wherein the activity is bioluminescence, siderophore production, type III secretion, or metalloprotease production.
 18. A method of inhibiting bacterial infection of a host comprising contacting the bacteria with the compound of claim 1, wherein the bacteria are Gram-negative quorum sensing bacteria.
 19. The method of claim 8 wherein the contacting is with a medical device that is coated with one or more of the compounds.
 20. The method of claim 19 wherein the medical device is a catheter.
 21. A method of disrupting detection of acyl-homoserine lactone-type autoinducer in Gram-negative bacteria comprising contacting the bacteria with a compound whose structure is


22. The method of claim 21 wherein the contacting comprises administering to a subject having a bacterial infection a therapeutically effective amount of the compound, wherein the bacteria is of a type that controls virulence factors by quorum sensing.
 23. The method of claim 21 wherein the bacteria are attached to a solid surface and the contacting comprises exposing the bacteria to a composition comprising the compound in an amount that affects biofilm formation.
 24. The method of claim 21 wherein the compound is applied to a surface in an amount that affects bacterial biofilm formation such that bacteria contacting the surface are inhibited from forming a biofilm.
 25. The method of claim 21 that inhibits bacterial pathogenicity, siderophore production, type III secretion, or metalloprotease production.
 26. A method of inhibiting bacterial infection of a host comprising contacting the bacteria with a compound whose structure is

wherein the bacteria are gram-negative quorum sensing bacteria. 